论文是
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
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部分数据代码是公开的 下载链接https://zenodo.org/record/4781590#.YSB40Hzivic
论文本地pdf 玉米Science.pdf
附件本地pdf abg5289_Hufford_SM.pdf
今天的推文我们来重复一下论文附件中的Figure S16
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没有找到论文中提供代码中用到的数据集NLR-violin-col.csv，论文中提供的数据集是NLR-violin4.csv
部分数据集如下
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首先是读取数据集
violin2<-read.table('NLR-violin4.csv', sep=',',header=F)
将第二列第三列转换成因子
violin2$V2 <- as.factor(violin2$V2)
violin2$V3 <- as.factor(violin2$V3)
最基本的小提琴图
library(ggplot2)
plot3 <- ggplot(violin2, aes(x=V2, y=V1)) +
geom_violin()
plot3
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在此基础上加一个表示平均值的点
plot3 +
stat_summary(fun=mean, geom="point", shape=23, size=2)
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在这个基础上再添加抖动的散点图
plot3 +
stat_summary(fun=mean, geom="point", shape=23, size=2)+
geom_jitter(position = position_jitter(height = .3,
width = .3),
aes(colour = factor(V3)),
size=0.5)
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自定义设置散点的颜色
plot3 +
stat_summary(fun=mean, geom="point", shape=23, size=2)+
geom_jitter(position = position_jitter(height = .3,
width = .3),
aes(colour = factor(V3)),
size=0.5) +
scale_colour_manual(name="colour",
values=c("goldenrod1",
"royalblue",
"gray47",
"orchid",
"orangered",
"limegreen",
"brown",
"darkgreen"))
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最后是更改x轴和y轴的标题和设置一个主题
plot3 +
stat_summary(fun=mean, geom="point", shape=23, size=2)+
geom_jitter(position = position_jitter(height = .3,
width = .3),
aes(colour = factor(V3)),
size=0.5) +
scale_colour_manual(name="colour",
values=c("goldenrod1",
"royalblue",
"gray47",
"orchid",
"orangered",
"limegreen",
"brown",
"darkgreen"))+
labs(x="NLR prediction", y="Copy Number of NLRs") +
theme_minimal()
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论文中提供的代码到这里就结束了，和最终附件中的图还是有些许差别的，接下来增加一些代码使之更像附件中的图
更改x轴刻度的文本,并将其设置为斜体
plot3 +
stat_summary(fun=mean, geom="point", shape=23, size=2)+
geom_jitter(position = position_jitter(height = .3,
width = .3),
aes(colour = factor(V3)),
size=0.5) +
scale_colour_manual(name="colour",
values=c("goldenrod1",
"royalblue",
"gray47",
"orchid",
"orangered",
"limegreen",
"brown",
"darkgreen"))+
labs(x="NLR prediction", y="Copy Number of NLRs") +
theme_minimal() +
scale_x_discrete(labels=c("A. thaliana",
"B. distachyon",
"Z. mays"))+
theme(axis.text.x = element_text(face="italic"))
image.png
更改图例的文字标签
plot3 +
stat_summary(fun=mean, geom="point", shape=23, size=2)+
geom_jitter(position = position_jitter(height = .3,
width = .3),
aes(colour = factor(V3)),
size=0.5) +
scale_colour_manual(name=NULL,
values=c("goldenrod1",
"royalblue",
"gray47",
"orchid",
"orangered",
"limegreen",
"brown",
"darkgreen"),
labels=c("Stiff stalk",
"Nonstiff stalk",
"Mixed",
"Popcorn",
"Sweetcorn",
"Tropical",
"Accessions",
"Accessions"))+
labs(x="NLR prediction", y="Copy Number of NLRs") +
theme_minimal() +
scale_x_discrete(labels=c("A. thaliana",
"B. distachyon",
"Z. mays"))+
theme(axis.text.x = element_text(face="italic"))
image.png
通过代码我只能做到这种程度了，如果需要完全模仿原图的图例目前只能借助其他工具编辑图片了
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今天推文的示例数据和代码可以在后台留言20211009获取